Goenrich Save

GO enrichment with python -- pandas meets networkx

Project README

goenrich

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Convenient GO enrichments from python. For use in python projects.

#. Builds the GO-ontology graph #. Propagates GO-annotations up the graph #. Performs enrichment test for all categories #. Performs multiple testing correction #. Allows for export to pandas for processing and graphviz for visualization

Installation

| Install package from pypi and download ontology and needed annotations.

.. code:: shell

pip install goenrich
mkdir db
# Ontology
wget http://purl.obolibrary.org/obo/go/go-basic.obo -O db/go-basic.obo
# UniprotACC
wget http://geneontology.org/gene-associations/goa_human.gaf.gz -O db/gene_association.goa_human.gaf.gz
# Yeast SGD
wget http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz -O db/gene_association.sgd.gz
# Entrez GeneID
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz -O db/gene2go.gz

Run GO enrichment

.. code:: python

import goenrich

build the ontology

O = goenrich.obo.ontology('db/go-basic.obo')

use all entrez geneid associations form gene2go as background

use annot = goenrich.read.goa('db/gene_association.goa_human.gaf.gz') for uniprot

use annot = goenrich.read.sgd('db/gene_association.sgd.gz') for yeast

gene2go = goenrich.read.gene2go('db/gene2go.gz')

use values = {k: set(v) for k,v in annot.groupby('go_id')['db_object_symbol']} for uniprot/yeast

values = {k: set(v) for k,v in gene2go.groupby('GO_ID')['GeneID']}

propagate the background through the ontology

background_attribute = 'gene2go' goenrich.enrich.propagate(O, values, background_attribute)

extract some list of entries as example query

use query = annot['db_object_symbol'].unique()[:20]

query = gene2go['GeneID'].unique()[:20]

for additional export to graphviz just specify the gvfile argument

the show argument keeps the graph reasonably small

df = goenrich.enrich.analyze(O, query, background_attribute, gvfile='test.dot')

generate html

df.dropna().head().to_html('example.html')

call to graphviz

import subprocess subprocess.check_call(['dot', '-Tpng', 'test.dot', '-o', 'test.png'])

Generate png image using graphviz:

.. code:: shell

dot -Tpng example.dot > example.png

or directly from python:

.. code:: python

import subprocess subprocess.check_call(['dot', '-Tpng', 'example.dot', '-o', 'example.png'])

.. image:: https://cloud.githubusercontent.com/assets/2606663/8525018/cad3a288-23fe-11e5-813c-bd205a47eed8.png

Check the documentation for all available parameters

Licence & Contributors

This work is licenced under the MIT licence

Contributions are welcome!

Special thanks

  • @lukauskas <https://github.com/lukauskas/>_ for implementing i/o support for file-like objects.
  • @zfrenchee <https://github.com/zfrenchee/>_ for fixing a bug in the calculation of the test statistic.
  • @pommy1 <https://github.com/pommy1/>_ for implementing support for networkx >= 2.0.0.

Building the documentation

.. code:: shell

sphinx-apidoc -f -o docs goenrich goenrich/tests

Open Source Agenda is not affiliated with "Goenrich" Project. README Source: jdrudolph/goenrich
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